DRAMP: a comprehensive data repository of antimicrobial peptides

Abstract

The growing problem of antibiotic-resistant microorganisms results in an urgent need for substitutes to conventional antibiotics with novel modes of action and effective activities. Antimicrobial peptides (AMPs), produced by a wide variety of living organisms acting as a defense mechanism against invading pathogenic microbes, are considered to be such promising alternatives. AMPs display a broad spectrum of antimicrobial activity and a low propensity for developing resistance. Therefore, a thorough understanding of AMPs is essential to exploit them as antimicrobial drugs. Considering this, we developed a comprehensive user-friendly data repository of antimicrobial peptides (DRAMP), which holds 17349 antimicrobial sequences, including 4571 general AMPs, 12704 patented sequences and 74 peptides in drug development. Entries in the database have detailed annotations, especially detailed antimicrobial activity data (shown as target organism with MIC value) and structure information. Annotations also include accession numbers crosslinking to Pubmed, Swiss-prot and Protein Data Bank (PDB). The website of the database comes with easy-to-operate browsing as well as searching with sorting and filtering functionalities. Several useful sequence analysis tools are provided, including similarity search, sequence alignment and conserved domain search (CD-Search). DRAMP should be a useful resource for the development of novel antimicrobial peptide drugs.

Figure 1. Architecture of the datasets in DRAMP.

“IdGeneralAMPs”, “IdClinicalAMPs” and “IdPatentAMPs” are storage structures of the General, Clinical and Patent dataset respectively. The General and Patent datasets fit into two subsets: natural peptides and synthetic peptides. Plant AMPs and bacteriocins belonging to natural AMPs are further stored as separate datasets. About half general peptides in DRAMP are available of MIC values along with target organisms and 253 general entries possess known structures.

Figure 2. Screenshots of DRAMP web interfaces.

(a) shows the advanced search page. This interface allows users to query database by a combination of various conditions; (b) shows the browse interface of DRAMP; (c) shows the result of query or browse; (d) shows the detailed information page; (e) shows integrated analysis tools in DRAMP.

Figure 3. Length distribution of natural antimicrobial peptides.

Every scatter indicates the percentage of natural AMPs calculated to have their length ranging from 1 to 100.

Figure 4. Hydrophobic content distribution in natural and synthetic AMPs.

The hydrophobic content is represented as a ratio between the total hydrophobic residues and the total amino acids in a peptide.

Figure 5. Basic amino acid distribution in natural and synthetic AMPs.

Figure 6. Activity distribution in natural AMPs.